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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtggagtcgtaatgtgaaggcgatgatttttttccagtatgttgttttctatcgtggtttttcagtttcgagcttctccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGACTGAAGACGACATTCCCATATTTCTGACTCTGAATATTGTACCTTGTTA

Basic information

species Zea mays
transcript GRMZM2G047860_T01
intron # 5
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|40337486|gb|CK371556.1|CK371556
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|60342892|gb|DN209865.1|DN209865
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|37400289|gb|CF637495.1|CF637495
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|33094100|gb|CF054094.1|CF054094
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|32936672|gb|CF041491.1|CF041491
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCCCTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|32917049|gb|CF021861.1|CF021861
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|211053628|gb|FL481081.1|FL481081
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|33103180|gb|CF063140.1|CF063140
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGTTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|32933985|gb|CF038797.1|CF038797
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|33104168|gb|CF064128.1|CF064128
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGTTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|32933645|gb|CF038457.1|CF038457
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|94472096|gb|EB701054.1|EB701054
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|116828198|gb|EC855483.1|EC855483
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|76014693|gb|DT941863.1|DT941863
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|86465815|gb|DY232188.1|DY232188
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCAGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|24767007|gb|CA402152.1|CA402152
EST:     TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA
EST: gi|32919256|gb|CF024068.1|CF024068
EST:     TTTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAG                         TTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTTTAGTTGCGTCGGA
genomic: TCTACGACAAAAACTACAGATACTAAACCAGTTCAAAATCCACTCAGCAGgtcagtggag ... tccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagtatgttgttttctatcgtggtttttcagtttcgagcttctccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGACTGAAGACGACATTCCCATATTTCTGACTCTGAATATTGTACCTTGTTA
                                         cttctcctt  CT-rich tract
             ttttctat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtggagtcgtaatgtgaaggcgatgatttttttccagtatgttgttttctatcgtggtttttcagtttcgagcttctccttgacagTTTGAAGATGACCTTGCTCACGAGCCTCATGCAAGCTATAGTTGCGTCGGACTGAAGACGACATTCCCATATTTCTGACTCTGAATATTGTACCTTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA